Dear Rosetta experts,
I have been using rosetta mainly for refinement and iterative local rebuilding into cryo-em densities at reolustions of ~3-3.5 Angstrom. I am wondering how (or if it is possible) to combine and complete a set of backbone fragments predicted by external software into a single backbone trace using rosetta. To make matters somewhat more complicated I would need to do this without any sequence information using only polyA fragments.
I can generate multiple backbone fragments from density alone using buccaneer. The fragments have a length of 5-25aas and a high local accuracy but poor overall correlation with the native structure. Superimposistion of all these fragments reveal that a "consensus" of structure could be quite accurate even without sequence information. I have looked at iterative RosettaCM modelling as described in the electron density refinement tutorial. This however seems to rely quire heavily on sequence alignment for merging and completeing models. I am not sure how I would, or if I could, implement this for a set of predicted polyA stretches.
The end goal would be to try to automate the intial chain tracing for large, multichain cryo-em structures where protein identity is determined from density alone.
Any help or insight would be appreciated.